Nothing
#Import data tab#####
dataimport.tab <- tabItem(
tabName = "dataimport",
importFilesOutput("import")
)
#####
#Heatmap tab#####
heatmap.tab <- tabItem(
tabName = "heatmap",
fluidPage(
fluidRow(
box(width=12, solidHeader = F, title = "Heatmap of lowest common ancestor annotations, based on selected filters", status = "primary",
fluidRow(
column(2,
box(width=12,
uiOutput("metadata_stratify_selection"),
uiOutput("annotation_count_selection"),
uiOutput("annotation_stratify_selection"),
prettySwitch("logtransform","Log10 transform")
)
),
column(10, align="center",
withSpinner(rbokehOutput("annot.heatmap", width = "50%", height = "800px"))
)
)
)
),
fluidRow(
box(width = 12, solidHeader = T, title = "Metadata Filter Settings",
status = "primary", collapsible = T, collapsed = F,
fluidPage(
DT::dataTableOutput("metadata_table")
)
)
),
fluidRow(
box(width = 12, solidHeader = T, title = "Annotation Filter Settings",
collapsible = T, collapsed = F, status = "warning",
column(12, align="center",
fluidPage(
DT::dataTableOutput("contig_table", width = "100%")
)
)
)
)
)
)
#####
#Seqinfo tab#####
seqinfo.tab <- tabItem(
tabName = "seqinfo",
fluidRow(
tabBox(width = 12,
tabPanel(title = "Annotation Table",
fluidPage(
column(2,
box(width=NULL,
h4("Applied filters:"),
uiOutput("filterInfo"),
br(),
downloadButton("downloadContig", "Download Selected Contigs"),
downloadButton("downloadAllContig", "Download All Filtered Contigs")
)
),
column(10,
annotationTableOutput("annot.table")
)
)
),
###
tabPanel(title = "Contig Information",
fluidPage(
fluidRow(
box(status = "primary",
width = 12,
solidHeader = T,
fluidRow(
column(6,
uiOutput("select.contig.current"),
uiOutput("contig.summary")
),
column(6,
uiOutput("orf.size.cutoff")
)
)
)
),
fluidRow(
box(width = 12,
column(12, align="center",
rbokehOutput("orfplot", width = "80%", height = "600px")
)
)
)
)
),
###
tabPanel(title = "ORF Information",
fluidPage(
fluidRow(
box(status = "primary",
width = 12,
solidHeader = T,
fluidRow(
column(6,
uiOutput("select.orf.current"),
uiOutput("orf.sequence"),
uiOutput("orf.sequence.type"),
actionButton("collect.orf","Collect ORFs")
),
column(6,
uiOutput("orf.slidingwindow.winsize"),
uiOutput("orf.slidingwindow.type"),
tags$img(src="http://www.jalview.org/help/html/misc/properties.gif", height = "250px")
)
)
)
),
fluidRow(
box(width = 12,
plotOutput("orf.slidingwindow")
)
)
)
),
###
tabPanel(title = "ORF Collection Table",
fluidPage(
fluidRow(
box(status = "primary",
width = 12,
solidHeader = T,
DT::dataTableOutput("orf.collection.table"),
uiOutput("download.seqtype"),
downloadButton('downloadFasta', 'Download Fasta'),
actionButton("clear.orf","Clear Collection")
)
)
)
)
)
)
)
#####
body <- dashboardBody(
tags$script(
"Shiny.addCustomMessageHandler(
'resetValue', function(variableName) {
Shiny.onInputChange(variableName, null);
}
);"
),
tabItems(
dataimport.tab,
heatmap.tab,
seqinfo.tab
)
)
sidebar <- dashboardSidebar(
a(href = "https://github.com/dnieuw/ViromeBrowser", target = "_blank", img(src="ViromeBrowser_logo.svg", align = "middle", width="100%")),
sidebarMenu(id = "sidebar",
menuItemOutput("importdata"),
menuItemOutput("heatmap"),
menuItemOutput("seqinfo")
),
tags$footer(
a(href = "https://www.compare-europe.eu/", target = "_blank", img(src="COMPARE_logo.png", width = "100%")),
style=paste0("position:absolute; align: center; bottom:0px; width:100%; height:",
"110px", "; color: white; padding: 5px;")
)
)
dashboardPage(skin = "green",
dashboardHeader(title = "ViromeBrowser"),
sidebar,
body
)
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